Variant report

Variant	rs2185885
Chromosome Location	chr4:2938419-2938420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:150)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:150 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2936416-2939933	GM18505	blood:	n/a	n/a
2	POLR2A	chr4:2936463-2940004	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:2938272-2939348	GM10847	blood:	n/a	n/a
4	POLR2A	chr4:2936427-2939614	Hela-S3	cervix:	n/a	n/a
5	TAL1	chr4:2937756-2938684	K562	blood:	n/a	n/a
6	SP1	chr4:2937714-2938509	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:2935540-2939822	Hela-S3	cervix:	n/a	n/a
8	MAX	chr4:2936301-2939648	HCT-116	colon:	n/a	n/a
9	ZNF384	chr4:2938123-2938547	GM12878	blood:	n/a	n/a
10	RELA	chr4:2937153-2939870	GM18505	blood:	n/a	n/a
11	SPI1	chr4:2938182-2938526	GM12878	blood:	n/a	n/a
12	CHD2	chr4:2937878-2939510	GM12878	blood:	n/a	n/a
13	MTA3	chr4:2936419-2940060	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:2936420-2939905	K562	blood:	n/a	n/a
15	POLR2A	chr4:2936475-2940008	GM12891	blood:	n/a	n/a
16	POLR2A	chr4:2937124-2940033	K562	blood:	n/a	n/a
17	SIN3AK20	chr4:2936414-2939621	HCT-116	colon:	n/a	n/a
18	POLR2A	chr4:2937075-2939631	H1-hESC	embryonic stem cell:	n/a	n/a
19	BCLAF1	chr4:2937706-2939670	GM12878	blood:	n/a	n/a
20	NFIC	chr4:2937695-2938668	GM12878	blood:	n/a	n/a
21	NFATC1	chr4:2936959-2939864	GM12878	blood:	n/a	n/a
22	JUND	chr4:2937092-2939655	HCT-116	colon:	n/a	n/a
23	POLR2A	chr4:2936428-2940062	K562	blood:	n/a	n/a
24	POLR2A	chr4:2936474-2938797	IMR90	lung:	n/a	n/a
25	POLR2A	chr4:2936942-2939390	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr4:2936392-2939634	HCT-116	colon:	n/a	n/a
27	POLR2A	chr4:2936273-2939674	MCF-7	breast:	n/a	n/a
28	BATF	chr4:2938406-2939380	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:2938268-2939626	Raji	blood:	n/a	n/a
30	POLR2A	chr4:2936425-2939503	HCT-116	colon:	n/a	n/a
31	POLR2A	chr4:2937759-2939502	K562	blood:	n/a	n/a
32	TBL1XR1	chr4:2937858-2939653	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:2936447-2940060	GM12892	blood:	n/a	n/a
34	RELA	chr4:2936499-2938801	GM12891	blood:	n/a	n/a
35	CHD2	chr4:2938417-2938727	K562	blood:	n/a	n/a
36	POLR2A	chr4:2938378-2939244	SK-N-SH	brain:	n/a	n/a
37	POU2F2	chr4:2937610-2938471	GM12891	blood:	n/a	n/a
38	POLR2A	chr4:2936481-2939398	PBDE	blood:	n/a	n/a
39	IKZF1	chr4:2937926-2939864	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:2936416-2940081	GM12878	blood:	n/a	n/a
41	ELF1	chr4:2938386-2939596	GM12878	blood:	n/a	n/a
42	MYC	chr4:2937183-2939811	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr4:2937058-2939858	K562	blood:	n/a	n/a
44	POLR2A	chr4:2937786-2938644	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr4:2936414-2940014	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:2936327-2940084	HL-60	blood:	n/a	n/a
47	POLR2A	chr4:2937183-2939836	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr4:2937883-2938604	SK-N-MC	brain:	n/a	n/a
49	MAX	chr4:2938060-2938487	K562	blood:	n/a	n/a
50	ATF2	chr4:2937210-2939919	GM12878	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2756410..2759745-chr4:2935120..2939466,6	K562	blood:
2	chr4:2830493..2833231-chr4:2936573..2940194,3	MCF-7	breast:
3	chr4:2937764..2938593-chr7:5569551..5570127,2	Hela-S3	cervix:
4	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
5	chr4:2793408..2795261-chr4:2937928..2940807,2	MCF-7	breast:
6	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
7	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:
8	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
9	chr4:2744637..2750348-chr4:2934999..2939149,7	MCF-7	breast:
10	chr4:2756586..2759605-chr4:2935863..2938872,4	K562	blood:
11	chr4:2845404..2847784-chr4:2938194..2940916,3	MCF-7	breast:
12	chr4:2936565..2939326-chr4:2970679..2973500,2	K562	blood:
13	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
14	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
15	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
16	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
17	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
18	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
19	chr18:3447926..3450158-chr4:2936583..2939331,2	MCF-7	breast:
20	chr12:104680883..104682793-chr4:2937932..2939461,2	MCF-7	breast:
21	chr4:2818330..2820965-chr4:2936129..2938646,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2937273-2939869	ENSG00000249673
2	lnc-ADD1-1	chr4:2937273-2938617	ENSG00000249673
3	lnc-ADD1-1	chr4:2937278-2939869	NR_015453
4	lnc-ADD1-1	chr4:2937273-2938617	ENSG00000249673.2

No data

Variant related genes	Relation type
MFSD10	TF binding region
NOP14-AS1	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000177426	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012365	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1242228	0.86[CHB][hapmap]
rs1263338	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1263339	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263342	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1263344	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1263345	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1263347	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263349	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263360	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12642795	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1419045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843452	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16843523	0.86[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs2051560	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071695	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2097081	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2237004	0.87[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2239728	0.87[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2282772	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282773	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282774	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285084	0.87[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2301374	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857866	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3775068	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3796469	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4690000	0.89[CEU][hapmap]
rs4690001	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs4690065	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4961	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4963	0.94[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964	0.87[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73189458	0.89[EUR][1000 genomes]
rs762847	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7664801	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2185885	HELT	trans	parietal	SCAN
rs2185885	ZFYVE28	cis	parietal	SCAN
rs2185885	DGKQ	cis	parietal	SCAN
rs2185885	ZNF732	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2936600-2939600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:2936800-2939000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:2937000-2938600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:2937000-2938600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr4:2937000-2938600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr4:2937000-2939000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:2937200-2938800	Flanking Active TSS	NH-A	brain
8	chr4:2937200-2939600	Flanking Active TSS	HMEC	breast
9	chr4:2937200-2939800	Transcr. at gene 5' and 3'	NHEK	skin
10	chr4:2937400-2938600	Enhancers	Spleen	Spleen
11	chr4:2937400-2938600	Flanking Active TSS	HSMM	muscle
12	chr4:2937400-2939000	Flanking Active TSS	Hela-S3	cervix
13	chr4:2937400-2939400	Weak transcription	Ovary	ovary
14	chr4:2937600-2938600	Enhancers	Adipose Nuclei	Adipose
15	chr4:2937600-2938600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:2937600-2938800	Enhancers	Brain Substantia Nigra	brain
17	chr4:2937600-2939000	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:2937600-2939000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr4:2937600-2939000	Genic enhancers	Fetal Stomach	stomach
20	chr4:2937600-2939000	Enhancers	Lung	lung
21	chr4:2937600-2939000	Enhancers	Pancreas	Pancrea
22	chr4:2937600-2939200	Enhancers	Liver	Liver
23	chr4:2937600-2939200	Enhancers	Fetal Heart	heart
24	chr4:2937600-2939200	Enhancers	Fetal Thymus	thymus
25	chr4:2937600-2939200	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr4:2937600-2939200	Flanking Active TSS	GM12878-XiMat	blood
27	chr4:2937600-2939600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr4:2937600-2939600	Enhancers	Stomach Mucosa	stomach
29	chr4:2937800-2938600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:2937800-2938600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:2937800-2938600	Enhancers	Fetal Brain Female	brain
32	chr4:2937800-2938800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:2937800-2938800	Weak transcription	Left Ventricle	heart
34	chr4:2937800-2939000	Weak transcription	Colonic Mucosa	Colon
35	chr4:2937800-2939200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:2937800-2939200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:2937800-2939200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr4:2937800-2939400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:2937800-2939400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:2937800-2939400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr4:2937800-2939400	Enhancers	Psoas Muscle	Psoas
44	chr4:2937800-2939400	Genic enhancers	NHLF	lung
45	chr4:2937800-2939600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:2937800-2939600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:2937800-2939600	Enhancers	NHDF-Ad	bronchial
48	chr4:2937800-2939800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:2937800-2940000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:2937800-2941800	Weak transcription	Small Intestine	intestine

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